The present invention is directed to a method and apparatus for accessing a site on a biological substrate. In particular, the present invention is directed to the use of multiple levels of fiducial marks to access a specific site on a biological substrate.
Biological substrates, including microarrays, biochips, biosensors, multi-well assay plates, cytology slides and microscope slides are used in connection with a variety of applications. For example, such biological substrates are useful in connection with life science, biotechnology, pharmaceutical, chemical, agriscience, and biomedical manufacturing, development and discovery applications, particularly in genomics, proteomics, cellomics (the micro-scale analysis of temporal and spatial interactions of cellular components with proteins, genes and exogenous biomaterials), diagnostics, and pathology in which microscopy and biological microchip technologies are used. As such technologies become more advanced, it is increasingly important to access or identify specific sites on a biological substrate with great accuracy and repeatability. However, existing systems or devices for providing access to specific sites on a biological substrate do not provide the precision and repeatability that is increasingly required.
In addition, existing devices for use in connection with biological substrates lack a flexible system for identifying particular areas on a biological substrate for later access. Therefore, the task of locating previously accessed sites is difficult. For example, some cell biology applications require the repeated examination of cell and tissue features over time. In particular, there is a need to allow technicians to review and validate the work of other technicians, and there is a need to track changes in the orientation, position, shape, movement and response of a cell attached to a treated substrate over time. However, current systems available for use in these applications are unable to accurately identify and record the location of specific cells and to facilitate the accurate and precise reexamination of specific cells over time. The inability of existing systems to allow specific cells to be reaccessed is particularly apparent where a substrate to which the cells are attached has been removed from and then reinserted into the device, or where a subsequent access operation is conducted using a device that is different from the device initially used to access the cells. The inability of existing devices to identify, record and communicate the accurate location of cells is a major barrier to the automation of such applications. Therefore, conventional systems require a time consuming, manual intervention by a knowledgeable user in order to locate the cell feature of interest during a time sequence study. Accordingly, the process is inefficient, and can be difficult to execute repeatedly. The process is also imprecise, resulting in a subjective process characterized by inherent variability.
Another application for systems capable of precisely positioning biological materials is found in connection with microarrays. Microarrays are sets of densely spaced, miniaturized chemical or biochemical reaction sites (or spots) on a microscope slide or other solid supports. Examples of microarrays include: DNA, protein, cell tissue, antibody, vaccine, and antiviral arrays. The reaction sites are typically arranged in an array or a grid pattern. The sites may be deposited on the substrate by contact printing using pins or capillaries, or non-contact printing using an inkjet, piezoelectric or magnetostrictive actuated microdispenser, micro-electro-mechanical systems (MEMS) microfluidics dispenser, or syringe solenoid liquid handling device. Information regarding the precise location of the grid and the grid nodes (i.e. the reaction sites) on the substrate is required to properly analyze the sites. The deposition of material in a grid or matrix facilitates large scale studies, such as: mapping complex biological pathways and systems; screening large numbers of drug targets and potential drug candidates; and performing genomic scans of biallelic markers for identifying disease and drug effect genes. However, conventional array deposition systems are not able to accurately identify and record the location of arrayed materials and to communicate this information to systems used for post-deposition array processing, readout, and analysis. Therefore, the full potential of microarrays has not yet been realized.
In a biochip or biosensor, one or more miniaturized chemical or biochemical reaction sites (or dots) are arranged in a pattern on a substrate. The precise location of the dots on the substrate are biochemically important, since the dots are deposited on preexisting features (or targets), such as activated surface sites or electrodes. If the dots do not precisely align with the preexisting features, the signal to noise ratio may be reduced, resulting in decreased sensitivity. Furthermore, it is important to produce uniform biochips in order to reduce variability in experimental procedures. However, existing devices are incapable of precisely depositing (or targeting) specific sites on a biochip or biosensor surface. Accordingly, the quality and uniformity of biochips and biosensors could be improved.
Therefore, while devices for accessing biological substrates have been developed, systems that provide access with desired levels of precision and repeatability have not been achieved. In addition, systems that provide for the convenient and accurate association of location information regarding a specific site or sites on a particular biological substrate with that substrate have not been achieved. Therefore, a need exists for a system capable of accessing sites on biological substrates with high levels of precision and repeatability. In addition, a need exists for a system that allows for the convenient and accurate association of information regarding a biological substrate with that substrate.
In accordance with the present invention, a method and an apparatus for accessing specific sites on a biological substrate with a high degree of precision and repeatability are provided. In addition, the present invention provides a method and an apparatus for associating information regarding a biological substrate with that substrate. The present invention allows predetermined sites to be targeted, and additionally allows previously accessed sites to be re-accessed. Accordingly, the present invention has applicability to both the creation of bioactive devices, including microarrays, biochips, and biosensors, and in re-accessing specific areas of a biological substrate on which a specimen is deposited. The present invention therefore has applicability to producing miniaturized and high precision devices utilizing biological materials, and to improving the accuracy and workload of lab technicians.
In accordance with an embodiment of the present invention, a device for accessing a site on a biological substrate is provided. The device utilizes more than one fiducial level system to orient an access device with respect to the biological substrate. Thus, a first fiducial level system may be utilized to establish a first fiducial level datum point, which may coincide to a biological substrate platform datum point. The first fiducial level system may be used for gross positioning of the biological substrate with respect to an access device (or vice versa). In addition, a second fiducial level system may be utilized to establish a second fiducial level datum point with respect to either the biological substrate platform datum point or the first fiducial level system datum point. The second fiducial level system may be used for fine positioning of the access device with respect to the biological substrate. In accordance with a further embodiment of the present invention, additional fiducial level systems may be provided. In addition, multiple instances of a fiducial level system may be provided. For example, a tray containing a plurality of biological substrates may include a second fiducial level system for each biological substrate.
In accordance with an embodiment of the present invention, the access device may include a readout unit, such as a microscope or scanner, or a material deposition unit. The access device may have a reference point or origin, and the position of that reference point with respect to a biological substrate platform datum point may be monitored. A device in accordance with an embodiment of the present invention may utilize sensors for determining the position of various fiducial level systems relative to the access device reference point using one or more sensors appropriate to the type of fiducial marks incorporated in the fiducial level systems. For instance, printed or inscribed fiducial marks may be apprehended by optical sensors. Accordingly, a device in accordance with the present invention may incorporate machine vision capabilities. According to another embodiment of the present invention, the device may utilize magnetic detectors for use in connection with magnetic fiducial marks or fluorescence detectors for use in connection with fluorescent fiducial marks.
Biological substrates that may be used in connection with the device of the present invention include microarrays, biochips, biosensors, multi-well assay plates, and biological sample or cytology slides, or any biological substrate that requires the accurate and precise locating of features below a few thousand microns in size. For instance, in connection with a microarray, which may provide a large number of wells or reaction sites arrayed over a single substrate, a device in accordance with the present invention may be utilized to accurately place biological materials in or remove biological material from the predefined wells or sites. Accordingly, the present invention allows specific sites to be targeted. The targeting capabilities of a device in accordance with the present invention are also useful in connection with the production of biochips, in which the precise deposition of biological material on one or more electrodes or on chemically treated sites is required. Similarly, the targeting of material in connection with biosensor applications is facilitated by the present invention. In connection with biological samples, such as cytology slides, the present invention allows particular cells on such a slide to be accessed quickly and conveniently, even after the slide has been removed from a device and reinserted, and even using different devices.
In a further aspect of the present invention, identifiers are associated with each substrate. These identifiers, which may include numeric or bar codes, allow information regarding the individual biological substrates to be stored in and retrieved from files identified or indexed by the associated identifier. Accordingly, information related to a particular biological substrate may be conveniently accessed by referencing a file or other subset of data associated with the assigned identifier. The identifier may be applied to a biological substrate prior to or following an access operation. In accordance with an embodiment of the present invention, the identifier is provided in the form of a printed label that can be adhered to the biological substrate. In accordance with still another embodiment of the present invention, the printed label includes, in addition to an identifier, fiducial marks included as part of one or more fiducial level systems.
The present invention additionally provides a method for facilitating the accessing of specific sites on a biological substrate with a high degree of precision and repeatability. In general, the method includes utilizing more than one fiducial level system for establishing datum points used to accurately record a location or to re-access a location on a biological substrate. In accordance with an embodiment of the present invention, a first fiducial level system is provided for coarse location and positioning. The first fiducial level system may be associated with a machine platform, with a biological substrate, or with a tray containing one or more biological substrates. In addition, a second fiducial level system is associated with a tray of biological substrates or with an individual biological substrate, and is used for relatively fine positioning operations. Additional fiducial level systems may also be provided.
During an accessing operation, a targeted location may be identified by reference to a fiducial level system associated with the biological substrate being accessed. For example, a particular site may be targeted by receiving location information entered by a user or retrieved from a file associated with the biological substrate by an identifier. Access operations involving a site on a biological substrate that is not predetermined may be carried out, and the precise location that was accessed recorded by reference to a fiducial level system. That information may be recorded in a file associated with the biological substrate by an identifier assigned to the biological substrate. The coordinates of a location on a biological substrate may be given with reference to a fiducial level system associated with the particular biological substrate. These coordinates may be translated into coordinates referenced to a datum point that is established with respect to a machine platform utilized in connection with accessing operations.
The present invention provides a method for standardizing various standalone devices or components of a multi-functional device with respect to accessing specific sites on a biological substrate with a high degree of precision and repeatability. In general, the method includes utilizing a fiducial level system for establishing datum points used to accurately record a location or to re-access a location on a biological substrate. In accordance with an embodiment of the present invention, fiducial level system information can be shared by any number of standalone devices or components of a multi-functional device for accessing specific sites on a biological substrate at any time over the entire lifetime of the substrate. The fiducial level system information associated with the biological substrate is accessed by the various devices acting upon the substrate by an identifier assigned to the biological substrate.
Additional advantages of the present invention will become readily apparent from the following discussion, particularly when taken together with the accompanying drawings.